5IXQ | pdb_00005ixq

Crystal structure of the Arabidopsis receptor kinase HAESA LRR ectdomain in complex with the peptide hormone IDA.

• PDB DOI: https://doi.org/10.2210/pdb5IXQ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2016-03-23 Released: 2016-04-20 
• Deposition Author(s): Santiago, J., Hothorn, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.207 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Mechanistic insight into a peptide hormone signaling complex mediating floral organ abscission.

Santiago, J., Brandt, B., Wildhagen, M., Hohmann, U., Hothorn, L.A., Butenko, M.A., Hothorn, M.

(2016) Elife 5

• PubMed: 27058169 
• DOI: https://doi.org/10.7554/eLife.15075
• Primary Citation Related Structures: 
  5IXO, 5IXQ, 5IXT, 5IYV, 5IYX


• PubMed Abstract: 
  

  Plants constantly renew during their life cycle and thus require to shed senescent and damaged organs. Floral abscission is controlled by the leucine-rich repeat receptor kinase (LRR-RK) HAESA and the peptide hormone IDA. It is unknown how expression of IDA in the abscission zone leads to HAESA activation. Here we show that IDA is sensed directly by the HAESA ectodomain. Crystal structures of HAESA in complex with IDA reveal a hormone binding pocket that accommodates an active dodecamer peptide. A central hydroxyproline residue anchors IDA to the receptor. The HAESA co-receptor SERK1, a positive regulator of the floral abscission pathway, allows for high-affinity sensing of the peptide hormone by binding to an Arg-His-Asn motif in IDA. This sequence pattern is conserved among diverse plant peptides, suggesting that plant peptide hormone receptors may share a common ligand binding mode and activation mechanism.

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Organizational Affiliation: 
• Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.
Department of Biosciences, Section for Genetic and Evolutionary Biology, University of Oslo, Oslo, Norway.
Institute of Biostatistics, Leibniz University, Hannover, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.33 kDa 
• Atom Count: 4,855 
• Modeled Residue Count: 607 
• Deposited Residue Count: 628 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-like protein kinase 5	A	616	Arabidopsis thaliana	Mutation(s): 0  Gene Names: RLK5, HAE, At4g28490, F21O9.180 EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for P47735 (Arabidopsis thaliana) Explore P47735  Go to UniProtKB:  P47735
Glycosylation
Glycosylation Sites: 7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein IDA	B	12	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q8LAD7 (Arabidopsis thaliana) Explore Q8LAD7  Go to UniProtKB:  Q8LAD7

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth A], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	J [auth A], K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP	B	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.207 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.282	α = 90
b = 148.282	β = 90
c = 57.93	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Santiago, J., Hothorn, M.

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary